Differential TDP-43 interactomes between the cortex and cerebellum in the mouse

TAR DNA binding protein 43 (TDP-43) is the core pathogenic protein across a spectrum of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, but its pathological deposition shows regional selectivity, with abundant TDP-43 positive aggregates in the frontal cortex and spinal cord, and a much lower burden in the cerebellum. In health, TDP-43 expression in the cerebellum is higher than in cortex, hence what underpins this differential vulnerability to TDP-43 aggregation is unclear. Here we demonstrate that in healthy C57Bl/6J mice not only is TDP-43 expression higher in the cerebellum than the cortex, but that this expression difference is driven primarily by differences in cytoplasmic load. Mass spectrometry analysis of TDP-43 pull downs from the cortex and cerebellum of healthy mice identified TDP-43 interactors across a number of core functional pathways, with numerous differences between the two brain regions. Data are available via ProteomeXchange with identifier PXD062532. Notably, there were more interactors identified in both nuclear and cytoplasmic fractions within the cortex than the cerebellum. Putative interactions with four core paraspeckle proteins; SFPQ, NONO, FUS and PSPC1 were confirmed using immunoprecipitation and western blot analysis. Follow up validation using proximity ligation assay showed abundant perinuclear cytoplasmic interactions between TDP-43 and all four paraspeckle proteins in both large motor cortex neurons and purkinje cells, with significantly reduced nuclear interactions detected in the motor cortex for SFPQ, FUS and PSPC1. These findings suggest that TDP-43-protein interactions markedly differ between the TDP-43 pathogenesis vulnerable cortex and relatively resistant cerebellum and exploring these differences may yield new insight into disease mechanisms within ALS/FTD.